Previously, regulators had pegged the shortfall at $600 million, or around 11 percent of MF’s $5.4 billion worth of brokerage accounts.

Yesterday’s shocking turn of events means that MF’s brokerage customers — some of whom rely on their MF accounts to meet monthly expenses — will face double the trouble when it comes to getting their money back.

MF’s bankruptcy took a scary turn when it emerged that millions in customer cash — money that was supposed to be separate, and therefore safe — went missing in MF’s frantic final days. The missing money is being probed by the FBI and Justice Department.

The bankruptcy trustee, James Giddens, said he still aims to give customers up to 60 percent of their money back. The remaining 40 percent, however, could take months or years to recover if at all.

“The customers want their money back, and they deserve their money back. But we can’t give what we don’t have,” Giddens’ spokesman Kent Jarrell told The Post.

“It’s horrible. It’s something that I just don’t understand,” said Rambod Poursalimi, whose retired 73-year-old father, Parviz, was relying on his $150,000 MF account to pay for medications and medical bills.

Poursalimi’s father had two-thirds of his nest egg tied up with MF — money “he can’t replace” because he no longer works, said Poursalimi.

Last week, bankruptcy judge Martin Glenn signed off on Giddens’ plan to return 60 percent, or $520 million, to customers in cash-only accounts — money that is on track to be distributed this week.

Early next month, Giddens aims to get approval to finish distributing the 60 percent to remaining commodity account customers.

Those distributions, estimated to total between $1.3 billion and $1.6 billion, will deplete the trustees’ available funds.

“The recordkeeping has been a problem,” Jarrell said in explaining the sudden doubling of the shortfall. “A lot of things happened quickly at the end (for MF) and unraveling it has not been an easy job.”